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From Short Reads to Chromosome-Scale Genome Assemblies

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Plant Pathogenic Fungi and Oomycetes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1848))

Abstract

A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.

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Acknowledgments

We would like to thank Sebastian Reyes-Chin-Wo (UC Davis) and Lida Derevnina (now The Sainsbury Laboratory, Norwich, UK) for their contributions in the initial setup of the workflow and William Palmer and Kelsey Wood (both UC Davis) for their reviews during preparation. We thank the UC Davis Bioinformatics Core for their computational and software support. We also thank Diane Saunders and members of her lab Guru Radhakrishnan, Daniel C.E. Bunting, and Antoine Persoons for their helpful comments. The work was supported by The Novozymes Inc. Endowed Chair in Genomics to RWM.

Conflicts of interest: The statements regarding Hi-C are based on experience resulting from collaboration with Dovetail Genomics. The authors declare that there are no other potential conflicts of interest.

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  1. The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA

    Kyle Fletcher & Richard Michelmore

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  1. Kyle Fletcher
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Correspondence to Richard Michelmore .

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  1. Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA

    Wenbo Ma

  2. Oregon State University, Corvallis, OR, USA

    Thomas Wolpert

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Fletcher, K., Michelmore, R. (2018). From Short Reads to Chromosome-Scale Genome Assemblies. In: Ma, W., Wolpert, T. (eds) Plant Pathogenic Fungi and Oomycetes. Methods in Molecular Biology, vol 1848. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8724-5_13

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